Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.
# 1.2 IDEOGRAM LABELS, TICKS, AND MODULARIZING CONFIGURATION # # In this tutorial, I will add tick marks, tick labels and ideogram # labels to the previous image. This will require the use of a <ticks> # block and expanding the <ideogram> block. # # To make the configuration more modular, the tick and ideogram # parameters will be stored in different files and imported using the # <<include>> directive. karyotype = data/karyotype/karyotype.human.txt # The chromosomes_unit value is used as a unit (suffix "u") to shorten # values in other parts of the configuration file. Some parameters, # such as ideogram and tick spacing, accept "u" suffixes, so instead of # # spacing = 10000000 # # you can write # # spacing = 10u # # See ticks.conf for examples. chromosomes_units = 1000000 <<include ideogram.conf>> <<include ticks.conf>> <image> <<include etc/image.conf>> </image> <<include etc/colors_fonts_patterns.conf>> <<include etc/housekeeping.conf>>
<ideogram> <spacing> default = 0.005r </spacing> # Ideogram position, fill and outline radius = 0.90r thickness = 20p fill = yes stroke_color = dgrey stroke_thickness = 2p # Minimum definition for ideogram labels. show_label = yes # see etc/fonts.conf for list of font names label_font = default label_radius = dims(image,radius) - 60p label_size = 30 label_parallel = yes </ideogram>
show_ticks = yes show_tick_labels = yes <ticks> radius = 1r color = black thickness = 2p # the tick label is derived by multiplying the tick position # by 'multiplier' and casting it in 'format': # # sprintf(format,position*multiplier) # multiplier = 1e-6 # %d - integer # %f - float # %.1f - float with one decimal # %.2f - float with two decimals # # for other formats, see http://perldoc.perl.org/functions/sprintf.html format = %d <tick> spacing = 5u size = 10p </tick> <tick> spacing = 25u size = 15p show_label = yes label_size = 20p label_offset = 10p format = %d </tick> </ticks>